Contacts of the strand formed by residues 874 - 881 (chain A) in PDB entry 5KZW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 874 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A LEU* 4.5 2.2 - - + -
858A PHE* 3.5 2.8 - - - -
859A TRP* 2.7 42.2 + - + +
873A TYR* 1.3 75.0 - - - +
875A GLN* 1.3 63.8 - - - +
876A VAL* 4.0 19.3 - - + -
891A ARG 3.3 12.3 - - - +
892A VAL* 4.2 8.1 - - + -
893A THR 3.0 20.8 + - - -
895A GLU 2.8 23.0 + - - -
896A GLY* 3.5 21.2 - - - +
899A LEU* 5.4 2.7 - - + -
943A MET* 5.9 0.9 - - + -
944A GLY* 5.3 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 875 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A HIS* 3.7 26.4 + - - -
715A GLN* 4.3 8.0 + - - -
856A GLU* 4.4 9.4 - - + +
857A LEU 3.3 11.7 - - - +
858A PHE* 4.7 4.1 - - + +
873A TYR* 3.9 26.9 + - + -
874A THR* 1.3 75.8 - - - +
876A VAL* 1.3 67.7 + - - +
877A ILE* 5.7 2.0 - - + -
890A VAL* 3.0 53.4 + - + +
891A ARG* 2.8 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 876 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A GLU* 3.2 5.9 - - - +
857A LEU* 2.9 38.9 + - + +
874A THR* 4.0 19.7 - - + -
875A GLN* 1.3 81.7 - - - +
877A ILE* 1.3 77.1 + - - +
878A PHE* 3.7 21.1 - - + -
887A ASN* 3.6 22.2 - - + +
888A GLU 3.5 7.9 - - - +
889A LEU* 4.3 9.6 - - + -
891A ARG 4.8 1.3 - - - +
892A VAL* 5.0 0.2 - - + -
943A MET* 3.6 25.4 - - + +
944A GLY* 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 877 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854A ARG* 3.7 35.4 - - - +
855A GLY 3.4 11.0 - - - +
856A GLU* 4.6 6.3 - - + +
875A GLN* 5.7 2.5 - - + -
876A VAL* 1.3 78.7 - - - +
878A PHE* 1.3 70.4 + - - +
879A LEU* 4.1 16.4 - - + -
887A ASN* 3.2 4.2 - - - -
888A GLU* 2.7 60.4 + - + +
890A VAL* 3.7 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 878 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A ILE* 3.7 24.7 - - + -
825A PRO* 4.6 4.5 - - + -
843A LEU* 3.8 37.2 - - + -
854A ARG* 3.3 5.4 - - - +
855A GLY 2.8 43.6 + - - +
856A GLU* 3.9 3.6 - - - -
857A LEU* 3.8 30.7 - - + -
876A VAL* 3.7 22.4 - - + -
877A ILE* 1.3 75.8 - - - +
879A LEU* 1.3 66.0 + - - +
885A ILE* 5.3 1.6 - - + -
886A VAL 3.4 4.3 - - - +
887A ASN* 4.0 13.0 - - + -
943A MET* 3.6 36.1 - - + -
947A PHE* 4.3 4.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 879 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A ILE* 4.0 2.9 - - - +
853A ALA 3.4 4.3 - - - +
854A ARG* 3.7 26.9 - - + +
877A ILE* 4.1 9.4 - - + -
878A PHE* 1.3 81.3 - - - +
880A ALA* 1.3 61.1 + - - +
881A ARG* 4.2 3.3 + - + -
884A THR* 3.9 1.0 + - - +
885A ILE* 3.4 2.4 - - - -
886A VAL* 2.9 51.8 + - + +
888A GLU* 3.7 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 880 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A ILE* 3.9 1.8 - - + +
845A VAL* 3.8 29.8 - - + -
847A LEU* 3.8 17.3 - - + -
851A GLY 3.6 2.2 - - - +
852A GLU* 3.4 7.4 - - - +
853A ALA* 2.8 32.7 + - + +
879A LEU* 1.3 74.3 - - - +
881A ARG* 1.3 63.8 + - - +
884A THR 3.2 9.2 - - - +
885A ILE* 3.9 8.1 - - + -
951A TRP* 5.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 881 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A GLY 3.4 7.5 + - - -
852A GLU* 3.0 41.4 + - - +
879A LEU* 4.2 3.5 + - + -
880A ALA* 1.3 77.1 - - - +
882A ASN* 1.3 81.7 + - + +
883A ASN 3.3 2.2 - - - -
884A THR* 2.9 31.6 + - - +
1013A NAG 6.2 3.1 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il